Si-scRNA-seq: Enabling ambient-stable single-cell transcriptomics through spatially confined biosilicification

Single-cell RNA sequencing (scRNA-seq) is constrained by rapid RNA degradation during sample storage, necessitating cold-chain logistics. Here we present spatially confined biosilicification (SCB), wherein RNA is encapsulated within a nanoscopic layer of amorphous silicon dioxide, as a highly effective methodology enabling ambient-temperature preservation of single-cell transcriptomes. By judiciously incorporating a silicification inhibitor, SCB achieves spatiotemporal control over both intra- and extracellular silica deposition, preventing excessive crosslinking and cell aggregation while preserving RNA biointegrity and accessibility. scRNA-seq performed with biosilicified cells (Si-scRNA-seq) maintained high transcriptomic fidelity with fresh samples (R² = 0.95 after 7 d) extending RNA half-life to 54.8 d at 25 °C, a 685-fold improvement compared to unprotected samples. Furthermore, Si-scRNA-seq confers robust resistance against oxidative and UV degradation. Compatible with mainstream platforms at ~0.1 RMB per sample, Si-scRNA-seq successfully resolves cellular heterogeneity in clinical lung, liver, and ovarian cancer specimens after extended room-temperature storage. Si-scRNA-seq provides a scalable and cold-chain-free solution for single-cell transcriptomics in research and clinical settings.